Meta-AMR-Plus

Introduction

Meta-AMR-Plus is a NextFlow pipeline designed for analyzing long-read Nanopore metagenomic data. It detects antimicrobial resistance (AMR) genes, identifies plasmids, and performs taxonomic classification using multiple tools and reference databases. The pipeline processes sequencing data efficiently and generates standardized output tables, making it easier to compare results across different tools and datasets.

Features

1. Read QC (FastQC)
2. Performs read pre-processing

• Adapter clipping and merging (porechop)
• Low complexity and quality filtering (Filtlong)
• Host-read removal (Minimap2)

3. Generates statistics for host-read removal using Samtools.
4. Performs optional genome assembly with Flye and assesses assembly quality using QUAST.
5. Optionally polishes the assembly using Racon.
6. Optionally downloads databases for AMR detection tools and PlasmidFinder if not provided by the user.
7. Performs AMR detection on assembled data using one or more of:

• ResFinder
• AMRFinderPlus
• CARD-RGI
• Abricate and
• ResFinder on unassembled reads.

8. Optionally performs hAMRonization to generate a comprehensive report integrating results from multiple AMR detection tools.
9. Performs plasmid detection assembled data using:

• PlasmidFinder
• PlasClass

10. Performs taxonomic classification using Centrifuge and Kaiju.
11. Generates visualizations for Centrifuge and Kaiju results using Krona.
12. Presents quality control and summary statistics for preprocessing, assembly, taxonomic classification, host-read removal, and AMR detection using ResFinder, AMRFinderPlus, CARD-RGI, and Abricate (MultiQC).

Usage

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

sample	fastq_1
sg17	sample17.fastq.gz
sg18	sample18.fastq.gz
sg19	sample19.fastq.gz

Each row represents a fastq file (single-end).

Additionally, you will need a database sheet that looks as follows:

samplesheet.csv:

tool	db_name	db_params	db_path
kaiju	kaiju_db		/<path>/<to>/kaiju_db
centrifuge	centrifuge_db		/<path>/<to>/centrifuge_database

The db_path column should point to directories or .tar.gz archives containing the databases required for the selected tools. For Kaiju and Centrifuge, pre-existing databases must be provided. For other tools, you can either provide the database path, or the pipeline will automatically generate the required database if not supplied.

Note

Abricate and PlasClass come with built-in databases, so no external database input is required for them.

Now, you can run the pipeline using:

nextflow run ./main.nf \
   -profile docker \
   --input samplesheet.csv \
   --databases database.csv \
   --outdir results \
   --perform_assembly \
   --perform_polish_assembly \
   --run_resfinder \
   --download_resfinder_db \

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page.

For more details about the output files and reports, please refer to the output documentation.

Credits

Meta-AMR-Plus was originally written by Leila Nasirzadeh.

We thank the following people for their contributions to the development of this pipeline: \

• Jyotirmoy Das \
• Debojyoti Das

Contributions and Support

Citations